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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caggcagattccatgcatacatgcgagctctcgccctacacccaccttccttaactcactgacgcgacccgccaccctgccgcccgccctcctgacacagAACATGGAGAACGTGGTGAACGACAACGACAACATCAAGCAAGACATGTCCATTGACGTGTACGGCCGCAAGAAGGCCGACGACTACGCCGCCAAACAG

Basic information

species Chlamydomonas reinhardtii
transcript EDP09628
intron # 4
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|7687461|gb|AW758107.1|AW758107
EST:     GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTG                         AACATGGAGAACGTGGTGAACGACAACGACAACATCAAGCAAGACATGTCC
genomic: GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTGgtgagaaacg ... cctgacacagAACATGGAGAACGTGGTGAACGACAACGACAACATCAAGCAAGACATGTCC
EST: gi|14227543|gb|BG846359.1|BG846359
EST:     GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTG                         AACATGGAGAACGTGGTGAACGACATCGACAACATCAAGCAAGACATGTCC
genomic: GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTGgtgagaaacg ... cctgacacagAACATGGAGAACGTGGTGAACGACAACGACAACATCAAGCAAGACATGTCC
EST: gi|161810931|gb|FC099684.1|FC099684
EST:     GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTG                         AACATGGAGAACGTGGTGAACGACAACGACAACATCAAGCAGGACATGTCC
genomic: GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTGgtgagaaacg ... cctgacacagAACATGGAGAACGTGGTGAACGACAACGACAACATCAAGCAAGACATGTCC
EST: gi|161802502|gb|FC091026.1|FC091026
EST:     GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTG                         AACATGGAGAACGTGGTGAACGACAACGACAACATCAAGCAGGACATGTCC
genomic: GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTGgtgagaaacg ... cctgacacagAACATGGAGAACGTGGTGAACGACAACGACAACATCAAGCAAGACATGTCC
EST: gi|15693543|gb|BI717848.1|BI717848
EST:     GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTG                         AACATGGAGAACGTGGTGAACGACNNACGACA-CATCAAGCAAGAC
genomic: GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTGgtgagaaacg ... cctgacacagAACATGGAGAACGTGGTGAACGACA-ACGACAACATCAAGCAAGAC
EST: gi|161815581|gb|FC101800.1|FC101800
EST:     GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTG                         AACATGGAGAACGTGGTGAACGACAACGACAACATCAAGCAGGACATGTCC
genomic: GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTGgtgagaaacg ... cctgacacagAACATGGAGAACGTGGTGAACGACAACGACAACATCAAGCAAGACATGTCC
EST: gi|161790768|gb|FC079471.1|FC079471
EST:     GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTG                         AACATGGAGAACGTGGTGAACGACAACGACAACATCAAGCAGGACATGTCC
genomic: GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTGgtgagaaacg ... cctgacacagAACATGGAGAACGTGGTGAACGACAACGACAACATCAAGCAAGACATGTCC
EST: gi|161819382|gb|FC109380.1|FC109380
EST:     GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTG                         AACATGGAGAACGTGGTGAACGACAACGACAACATCAAGCAGGACATGTCC
genomic: GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTGgtgagaaacg ... cctgacacagAACATGGAGAACGTGGTGAACGACAACGACAACATCAAGCAAGACATGTCC
EST: gi|161797004|gb|FC087091.1|FC087091
EST:     GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTG                         AACATGGAGAACGTGGTGAACGACAACGACAACATCAAGCAGGACATGTCC
genomic: GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTGgtgagaaacg ... cctgacacagAACATGGAGAACGTGGTGAACGACAACGACAACATCAAGCAAGACATGTCC
EST: gi|161802748|gb|FC092455.1|FC092455
EST:     GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTG                         AACATGGAGAACGTGGTGAACGACAACGACAACATCAAGCAGGACATGTCC
genomic: GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTGgtgagaaacg ... cctgacacagAACATGGAGAACGTGGTGAACGACAACGACAACATCAAGCAAGACATGTCC
EST: gi|23362806|gb|BU650626.1|BU650626
EST:     GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTG                         AACATGGAGAACGTGGTGAACGACAACGACAACATCAAGCAAGACATGTCC
genomic: GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTGgtgagaaacg ... cctgacacagAACATGGAGAACGTGGTGAACGACAACGACAACATCAAGCAAGACATGTCC
EST: gi|15372656|gb|BI532082.1|BI532082
EST:     GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTG                         AACATGGAGAACGTGGTGAACGACAACGANNCA-CATCAAGCA
genomic: GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTGgtgagaaacg ... cctgacacagAACATGGAGAACGTGGTGAACGACAACGA--CAACATCAAGCA
EST: gi|14225592|gb|BG844408.1|BG844408
EST:     GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTG                         AACATGGAGAACGTGGTGAACGACCACGAC
genomic: GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTGgtgagaaacg ... cctgacacagAACATGGAGAACGTGGTGAACGACAACGAC
EST: gi|161794759|gb|FC077357.1|FC077357
EST:     GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTG                         AACATGGAGAACGTGGTGAACGACAACGACAACATCAAGCAGGACATGTCC
genomic: GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTGgtgagaaacg ... cctgacacagAACATGGAGAACGTGGTGAACGACAACGACAACATCAAGCAAGACATGTCC
EST: gi|161812718|gb|FC094270.1|FC094270
EST:     GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTG                         AACATGGAGAACGTGGTGAACGACAACGACAACATCAAGCAGGACATGTCC
genomic: GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTGgtgagaaacg ... cctgacacagAACATGGAGAACGTGGTGAACGACAACGACAACATCAAGCAAGACATGTCC
EST: gi|161797930|gb|FC087419.1|FC087419
EST:     GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTG                         AACATGGAGAACGTGGTGAACGACAACGACAACATCAAGCAGGACATGTCC
genomic: GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTGgtgagaaacg ... cctgacacagAACATGGAGAACGTGGTGAACGACAACGACAACATCAAGCAAGACATGTCC
EST: gi|161801979|gb|FC088800.1|FC088800
EST:     GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTG                         AACATGGAGAACGTGGTGAACGACAACGACAACATCAAGCAGGACATGTCC
genomic: GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTGgtgagaaacg ... cctgacacagAACATGGAGAACGTGGTGAACGACAACGACAACATCAAGCAAGACATGTCC
EST: gi|23366045|gb|BU653865.1|BU653865
EST:     GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGNAGGACAAGCGCGTGCTG                         AACATGGAGAACGTGGTGAACGACAACGACCACATCAAGNCA-GACATGTC
genomic: GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTGgtgagaaacg ... cctgacacagAACATGGAGAACGTGGTGAACGACAACGACAACATCAAG-CAAGACATGTC
EST: gi|15697973|gb|BI722278.1|BI722278
EST:     GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTG                         AACATGGAGAACGTGGTGAACGACAACGANCA-CATCAAGCAAGACATGTC
genomic: GCAAGAGCCGCAGCAACTTCAACTTCAGCCTGGAGGACAAGCGCGTGCTGgtgagaaacg ... cctgacacagAACATGGAGAACGTGGTGAACGACAACGA-CAACATCAAGCAAGACATGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttccttaactcactgacgcgacccgccaccctgccgcccgccctcctgacacagAACATGGAGAACGTGGTGAACGACAACGACAACATCAAGCAAGACATGTCCATTGACGTGTACGGCCGCAAGAAGGCCGACGACTACGCCGCCAAACAG
                                            tcctgac  putative branch site (score: 2)
                                  ccgcccgccctcct  CT-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caggcagattccatgcatacatgcgagctctcgccctacacccaccttccttaactcactgacgcgacccgccaccctgccgcccgccctcctgacacagAACATGGAGAACGTGGTGAACGACAACGACAACATCAAGCAAGACATGTCCATTGACGTGTACGGCCGCAAGAAGGCCGACGACTACGCCGCCAAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
-aggcaga
- - - - - - - - atacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - aactcac